Petridis, Loukas wrote:
Hi,
We are examining a system comprising of two molecules (called mol1 and mol2) in
water that are initially separated by > 1.5nm. We calculate the surface
accessible area of the first molecule ( mol1) in two ways:
(a) sasa_a: by setting both the output and calculation groups to mol 1
(b) sasa_b: setting the calculation group to mol1 and mol2, and output group to mol1
During the simulation, the molecules are separated by more 1.5nm and since the
probe radius = 0.14nm, we expected the values of the two surface areas to be
identical. Instead we found sasa_a and sasa_b to differ by about +- 1.5 nm^2.
Although this variation is small compared to the mean value ~86 nm^2, it has
caused us some concern. We were also surprised that sasa_b was larger than
sasa_a for part of the simulation. (The same trend is observed when the
accuracy of the calculation was increased by using ndots=48).
I was wondering if anyone has some insight on why the two sasa values are not
identical.
From g_sas -h:
"The calculation group should always consists of all the non-solvent atoms in
the system. The output group can be the whole or part of the calculation group."
So, setting the calculation group to only include "mol1" is simply incorrect
usage of the program.
-Justin
I am attaching a figure displaying the calculations described above, obtained
by:
g_sas -f /traj-0-37 -s top.tpr -n index-1-2.ndx -b 0 -e 100 -ndots 24
Many thanks for your help,
Loukas
Loukas Petridis
Post-doctoral Research Fellow
Center for Molecular Biophysics, Oak Ridge National Laboratory
Building 6011, MS 6309, Oak Ridge, TN 37831
865-576-2576
http://cmb.ornl.gov/people/lpk
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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